Mortality levels attributed to infectious salmon anaemia viral (ISAV) infections were examined at the net pen and site level in the 1996 smolt year class in three areas of New Brunswick, Canada. The year class in this region was the first known to have potential exposure to ISAV beginning at the time of seawater transfer. There was considerable variability in mortality patterns among net pen groups of fish. Net pen outbreak definitions were based on at least seven high mortality days in which there were at least 100 per 100 000 fish per day or >5% cumulative mortality for the study period. There were 106 net pen outbreaks in a study population consisting of 218 net pens. Although the number of new cases decreased as water temperature decreased, overall mortality levels at the study sites did not decrease noticeably. The median peak daily mortality rate during outbreaks was 492 per 100 000 fish per day, with 10% of cases experiencing >5200 mortalities per 100 000 fish per day. The median duration of outbreaks in net pens for which the fish were not slaughtered during the outbreak was 33 days and the median total loss in those outbreaks was 6600 per 100 000 fish.